Variant report

Variant	rs2267666
Chromosome Location	chr6:35370728-35370729
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35364935..35367587-chr6:35369436..35372009,4	K562	blood:
2	chr6:35368369..35371007-chr6:35374165..35376691,3	K562	blood:
3	chr6:35369022..35371530-chr6:35380488..35382015,2	MCF-7	breast:
4	chr6:35358414..35360347-chr6:35370007..35371734,2	MCF-7	breast:
5	chr6:35307588..35310210-chr6:35369138..35372365,3	K562	blood:
6	chr6:35369456..35371995-chr6:35391240..35394220,2	MCF-7	breast:
7	chr6:35364935..35367619-chr6:35369623..35372118,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1040436	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1053049	0.93[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1883322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016520	0.88[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038067	0.97[CHD][hapmap];0.80[GIH][hapmap]
rs2038068	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076166	0.91[CHD][hapmap]
rs2076167	0.95[CEU][hapmap];0.88[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076168	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076169	0.86[CHD][hapmap]
rs2267665	0.91[CHD][hapmap]
rs2267667	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267668	0.88[CHD][hapmap]
rs2267669	0.90[CHD][hapmap]
rs2395622	0.89[ASN][1000 genomes]
rs2395623	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3734254	0.82[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4713858	0.86[CHD][hapmap]
rs6457818	0.82[ASN][1000 genomes]
rs760783	0.88[CHD][hapmap]
rs7749160	0.88[CHD][hapmap]
rs7751481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462082	0.88[CHD][hapmap]
rs9462083	0.83[ASN][1000 genomes]
rs9462084	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2267666	TULP1	cis	parietal	SCAN
rs2267666	DEF6	cis	multi-tissue	Pritchard

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35338400-35378400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:35345600-35378400	Weak transcription	Aorta	Aorta
3	chr6:35354000-35372400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:35359800-35378800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:35360000-35378200	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:35360000-35378400	Weak transcription	HSMMtube	muscle
7	chr6:35360000-35379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:35360000-35382600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:35360400-35372000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:35360400-35372200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:35360600-35372400	Weak transcription	Brain Anterior Caudate	brain
12	chr6:35360600-35378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:35361000-35378000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:35361000-35378600	Weak transcription	Adipose Nuclei	Adipose
15	chr6:35361000-35378600	Weak transcription	NHLF	lung
16	chr6:35361000-35378800	Weak transcription	Psoas Muscle	Psoas
17	chr6:35361200-35376200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:35361200-35378600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:35361800-35385800	Weak transcription	Small Intestine	intestine
20	chr6:35362000-35378000	Weak transcription	Spleen	Spleen
21	chr6:35362200-35378400	Weak transcription	Primary B cells from cord blood	blood
22	chr6:35362200-35378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:35362200-35380000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:35363400-35378200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:35363800-35371600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:35364000-35378000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:35365400-35375800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:35365400-35378600	Weak transcription	NHDF-Ad	bronchial
29	chr6:35365800-35377800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:35365800-35378600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:35365800-35378600	Weak transcription	Ovary	ovary
32	chr6:35366200-35378000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:35366200-35386800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:35366400-35382800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:35366600-35376600	Weak transcription	K562	blood
36	chr6:35366600-35378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:35367800-35371000	Enhancers	HMEC	breast
38	chr6:35367800-35371600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:35367800-35372800	Strong transcription	Primary T cells from cord blood	blood
40	chr6:35367800-35378600	Weak transcription	Thymus	Thymus
41	chr6:35368000-35371000	Enhancers	Duodenum Mucosa	Duodenum
42	chr6:35368000-35372000	Enhancers	Fetal Heart	heart
43	chr6:35368000-35372000	Enhancers	Pancreas	Pancrea
44	chr6:35368000-35372600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr6:35368200-35371000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:35368200-35371200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr6:35368200-35371200	Enhancers	Stomach Mucosa	stomach
48	chr6:35368600-35370800	Enhancers	Lung	lung
49	chr6:35368600-35371600	Enhancers	Left Ventricle	heart
50	chr6:35369000-35371000	Enhancers	Rectal Mucosa Donor 31	rectum

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